Razor,
I second Qavion's recommendation of the Big Boeing User's Guide. Not something you want to use when you are first learning the "box", but definitely good reading once you are in the seat. The authors will give you an example clearance, and then justify why their way to skin the cat is better than the other 5 options.
If you can find a way to get a software copy of a program called AEROSIM, that is a pretty decent interactive program that allows you to fly the airplane using the MCP and FMS. We use it to help bring students up to speed before they hit the sim. Good results. - BoxProf